Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 18:16:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/04_2023/7wly_32594.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 18219 2.51 5 N 4722 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 847": "NH1" <-> "NH2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 39": "OD1" <-> "OD2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 1": "OD1" <-> "OD2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 39": "OD1" <-> "OD2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28550 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8196 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 57, 'TRANS': 993} Chain breaks: 7 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8090 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 8225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8225 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 962 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "X" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.92, per 1000 atoms: 0.52 Number of scatterers: 28550 At special positions: 0 Unit cell: (132.834, 170.352, 202.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 5480 8.00 N 4722 7.00 C 18219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN C 165 " " NAG E 1 " - " ASN C 234 " Time building additional restraints: 11.24 Conformation dependent library (CDL) restraints added in 4.0 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6770 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 64 sheets defined 22.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.807A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.640A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.803A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.298A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.843A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.106A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.130A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.079A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.531A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.936A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.667A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.231A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.176A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 removed outlier: 3.622A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 3.951A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.766A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.712A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.524A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.568A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.773A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.586A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.564A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.925A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 719 removed outlier: 6.604A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.664A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.901A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.583A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC4, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.528A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.844A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.605A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.886A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.818A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.657A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.707A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.531A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.506A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE5, first strand: chain 'C' and resid 187 through 190 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.676A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 318 through 319 removed outlier: 4.265A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.967A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.541A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.586A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 565 through 567 removed outlier: 6.169A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.735A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.918A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.682A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'P' and resid 45 through 51 removed outlier: 5.631A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.598A pdb=" N ALA O 19 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.506A pdb=" N LEU O 11 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP O 110 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG7, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'Y' and resid 45 through 51 removed outlier: 5.640A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.572A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.89 Time building geometry restraints manager: 11.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7373 1.33 - 1.45: 6212 1.45 - 1.58: 15464 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29214 Sorted by residual: bond pdb=" N ILE A 805 " pdb=" CA ILE A 805 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N VAL Y 100 " pdb=" CA VAL Y 100 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N VAL B 445 " pdb=" CA VAL B 445 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N ARG B 237 " pdb=" CA ARG B 237 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 29209 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.12: 791 106.12 - 113.16: 15829 113.16 - 120.20: 10474 120.20 - 127.24: 12411 127.24 - 134.27: 254 Bond angle restraints: 39759 Sorted by residual: angle pdb=" N TYR C 449 " pdb=" CA TYR C 449 " pdb=" C TYR C 449 " ideal model delta sigma weight residual 113.61 105.41 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 112.89 106.42 6.47 1.24e+00 6.50e-01 2.72e+01 angle pdb=" C GLU B 702 " pdb=" CA GLU B 702 " pdb=" CB GLU B 702 " ideal model delta sigma weight residual 110.06 117.19 -7.13 1.39e+00 5.18e-01 2.63e+01 angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" CB ALA A 163 " ideal model delta sigma weight residual 110.77 102.42 8.35 1.63e+00 3.76e-01 2.62e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.40e+01 ... (remaining 39754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15904 17.82 - 35.65: 982 35.65 - 53.47: 177 53.47 - 71.30: 45 71.30 - 89.12: 20 Dihedral angle restraints: 17128 sinusoidal: 6596 harmonic: 10532 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -158.82 72.82 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 162.17 -69.17 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -42.47 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4282 0.111 - 0.221: 280 0.221 - 0.332: 9 0.332 - 0.442: 3 0.442 - 0.553: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 4573 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A1305 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C1301 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.342 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C7 NAG B1308 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.119 2.00e-02 2.50e+03 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3196 2.75 - 3.28: 29340 3.28 - 3.82: 45696 3.82 - 4.36: 54866 4.36 - 4.90: 94100 Nonbonded interactions: 227198 Sorted by model distance: nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.207 2.440 nonbonded pdb=" OG SER C 112 " pdb=" O PHE C 133 " model vdw 2.225 2.440 nonbonded pdb=" O TYR A 313 " pdb=" OG SER A 596 " model vdw 2.237 2.440 nonbonded pdb=" O THR C 676 " pdb=" OG1 THR C 676 " model vdw 2.264 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.269 2.440 ... (remaining 227193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 136 or (resid 137 and (name N or name CA o \ r name C or name O or name CB )) or resid 138 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 172 or (re \ sid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ rough 176 or (resid 177 through 178 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 227 or (resid 228 through 229 and (name N or n \ ame CA or name C or name O or name CB )) or resid 230 through 269 or (resid 270 \ through 271 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 2 through 334 or (resid 335 and (name N or name CA or name C or name O or name C \ B )) or resid 336 through 392 or (resid 393 through 394 and (name N or name CA o \ r name C or name O or name CB )) or resid 395 through 402 or (resid 403 and (nam \ e N or name CA or name C or name O or name CB )) or resid 404 through 461 or (re \ sid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 th \ rough 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) \ or resid 504 through 516 or (resid 517 through 518 and (name N or name CA or na \ me C or name O or name CB )) or resid 519 through 522 or (resid 523 and (name N \ or name CA or name C or name O or name CB )) or resid 524 through 527 or (resid \ 528 through 529 and (name N or name CA or name C or name O or name CB )) or resi \ d 530 through 532 or (resid 533 and (name N or name CA or name C or name O or na \ me CB )) or resid 534 through 550 or (resid 551 and (name N or name CA or name C \ or name O or name CB )) or resid 552 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 622 or \ resid 632 through 827 or (resid 828 through 829 and (name N or name CA or name \ C or name O or name CB )) or resid 830 through 978 or (resid 979 and (name N or \ name CA or name C or name O or name CB )) or resid 980 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 990 and (name N or name CA or name C or name O or name \ CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or name C or \ name O or name CB )) or resid 995 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 through 113 or \ (resid 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 205 or (re \ sid 206 and (name N or name CA or name C or name O or name CB )) or resid 207 th \ rough 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 through 334 or (resid 335 and (name N or name CA or name C or name \ O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 370 or (re \ sid 371 through 372 and (name N or name CA or name C or name O or name CB )) or \ resid 373 through 402 or (resid 403 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 426 or (resid 427 and (name N \ or name CA or name C or name O or name CB )) or resid 428 through 454 or (resid \ 455 and (name N or name CA or name C or name O or name CB )) or resid 456 throug \ h 516 or (resid 517 through 518 and (name N or name CA or name C or name O or na \ me CB )) or resid 519 through 827 or (resid 828 through 829 and (name N or name \ CA or name C or name O or name CB )) or resid 830 through 984 or (resid 985 and \ (name N or name CA or name C or name O or name CB )) or resid 986 through 1126 o \ r (resid 1127 and (name N or name CA or name C or name O or name CB )) or resid \ 1128 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 120 or (resid 121 a \ nd (name N or name CA or name C or name O or name CB )) or resid 122 through 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 through 142 or (resid 158 through 159 and (name N or name CA or name C or n \ ame O or name CB )) or resid 160 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 through 176 or (resid 177 throu \ gh 178 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 205 or (resid 206 and (name N or name CA or name C or name O or name CB )) \ or resid 207 through 227 or (resid 228 through 229 and (name N or name CA or nam \ e C or name O or name CB )) or resid 230 through 269 or (resid 270 through 271 a \ nd (name N or name CA or name C or name O or name CB )) or resid 272 through 345 \ or (resid 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 356 or (resid 357 and (name N or name CA or name C or name O or nam \ e CB )) or resid 358 through 370 or (resid 371 through 372 and (name N or name C \ A or name C or name O or name CB )) or resid 373 through 408 or (resid 409 and ( \ name N or name CA or name C or name O or name CB )) or resid 410 through 426 or \ (resid 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ through 454 or (resid 455 and (name N or name CA or name C or name O or name CB \ )) or resid 456 through 517 or (resid 518 and (name N or name CA or name C or n \ ame O or name CB )) or resid 519 through 522 or (resid 523 and (name N or name C \ A or name C or name O or name CB )) or resid 524 through 532 or (resid 533 and ( \ name N or name CA or name C or name O or name CB )) or resid 534 through 550 or \ (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 622 or resid 632 through 836 or resid 848 t \ hrough 987 or (resid 988 through 990 and (name N or name CA or name C or name O \ or name CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or n \ ame C or name O or name CB )) or resid 995 through 1147 or resid 1301 through 13 \ 09)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'O' selection = chain 'X' } ncs_group { reference = chain 'P' selection = (chain 'Y' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 130)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.710 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 74.840 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 29214 Z= 0.461 Angle : 0.859 12.650 39759 Z= 0.549 Chirality : 0.058 0.553 4576 Planarity : 0.012 0.297 5108 Dihedral : 12.275 89.124 10229 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3565 helix: -0.05 (0.19), residues: 730 sheet: -1.76 (0.18), residues: 856 loop : -2.37 (0.12), residues: 1979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 9 residues processed: 310 average time/residue: 0.3898 time to fit residues: 196.9361 Evaluate side-chains 178 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 3.080 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2388 time to fit residues: 8.2574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 0.0980 chunk 109 optimal weight: 40.0000 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 321 GLN A 370 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 804 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN A1058 HIS A1106 GLN A1135 ASN B 218 GLN B 239 GLN B 314 GLN B 580 GLN B 751 ASN B 779 GLN B 804 GLN B 955 ASN B1101 HIS C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 690 GLN C 751 ASN C 960 ASN C 965 GLN C1113 GLN C1135 ASN O 98 GLN Y 13 GLN Y 39 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 29214 Z= 0.177 Angle : 0.608 12.592 39759 Z= 0.308 Chirality : 0.046 0.282 4576 Planarity : 0.004 0.056 5108 Dihedral : 4.560 22.916 3890 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3565 helix: 0.85 (0.19), residues: 725 sheet: -1.48 (0.17), residues: 878 loop : -2.04 (0.13), residues: 1962 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 201 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 21 residues processed: 245 average time/residue: 0.3754 time to fit residues: 153.2716 Evaluate side-chains 188 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 3.182 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2614 time to fit residues: 14.6618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 272 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 327 optimal weight: 0.8980 chunk 353 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 324 optimal weight: 0.9980 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 29214 Z= 0.183 Angle : 0.569 12.223 39759 Z= 0.286 Chirality : 0.044 0.273 4576 Planarity : 0.004 0.053 5108 Dihedral : 4.407 21.860 3890 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3565 helix: 1.05 (0.20), residues: 734 sheet: -1.33 (0.17), residues: 876 loop : -1.82 (0.13), residues: 1955 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 20 residues processed: 242 average time/residue: 0.3927 time to fit residues: 159.0150 Evaluate side-chains 184 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 3.493 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2667 time to fit residues: 14.8049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 347 optimal weight: 0.0170 chunk 171 optimal weight: 0.9980 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 317 ASN B 437 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 935 GLN P 35 HIS P 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 29214 Z= 0.236 Angle : 0.576 9.816 39759 Z= 0.289 Chirality : 0.045 0.335 4576 Planarity : 0.004 0.055 5108 Dihedral : 4.432 40.407 3890 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3565 helix: 1.08 (0.20), residues: 737 sheet: -1.17 (0.17), residues: 889 loop : -1.72 (0.13), residues: 1939 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 176 time to evaluate : 3.329 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 31 residues processed: 218 average time/residue: 0.3720 time to fit residues: 136.6968 Evaluate side-chains 192 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 3.386 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2685 time to fit residues: 20.1720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 2.9990 chunk 197 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 30.0000 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 0.8980 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 218 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN O 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 29214 Z= 0.266 Angle : 0.574 9.625 39759 Z= 0.291 Chirality : 0.045 0.280 4576 Planarity : 0.004 0.055 5108 Dihedral : 4.434 34.198 3890 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3565 helix: 1.12 (0.20), residues: 730 sheet: -1.07 (0.18), residues: 877 loop : -1.66 (0.13), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 3.512 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 14 residues processed: 211 average time/residue: 0.3837 time to fit residues: 139.3053 Evaluate side-chains 173 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 159 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2965 time to fit residues: 12.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 5.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 348 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A1010 GLN B 544 ASN B1088 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 29214 Z= 0.209 Angle : 0.556 10.407 39759 Z= 0.279 Chirality : 0.044 0.313 4576 Planarity : 0.004 0.053 5108 Dihedral : 4.361 37.816 3890 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 1.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.14), residues: 3565 helix: 1.25 (0.20), residues: 735 sheet: -0.97 (0.18), residues: 859 loop : -1.58 (0.13), residues: 1971 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 3.376 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 197 average time/residue: 0.3718 time to fit residues: 124.6020 Evaluate side-chains 170 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 3.303 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2612 time to fit residues: 10.9126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 293 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 29214 Z= 0.169 Angle : 0.545 10.802 39759 Z= 0.272 Chirality : 0.044 0.266 4576 Planarity : 0.004 0.051 5108 Dihedral : 4.242 38.764 3890 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3565 helix: 1.39 (0.20), residues: 732 sheet: -0.84 (0.18), residues: 868 loop : -1.50 (0.14), residues: 1965 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 185 average time/residue: 0.3858 time to fit residues: 121.8367 Evaluate side-chains 163 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 155 time to evaluate : 3.581 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2841 time to fit residues: 9.1674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 220 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 29214 Z= 0.231 Angle : 0.564 10.519 39759 Z= 0.284 Chirality : 0.045 0.277 4576 Planarity : 0.004 0.049 5108 Dihedral : 4.324 37.300 3890 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3565 helix: 1.31 (0.20), residues: 731 sheet: -0.73 (0.18), residues: 865 loop : -1.52 (0.14), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 177 average time/residue: 0.4005 time to fit residues: 120.5398 Evaluate side-chains 163 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 154 time to evaluate : 3.539 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2776 time to fit residues: 9.5646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 20.0000 chunk 332 optimal weight: 50.0000 chunk 303 optimal weight: 3.9990 chunk 323 optimal weight: 50.0000 chunk 194 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 305 optimal weight: 0.0020 chunk 322 optimal weight: 8.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 29214 Z= 0.250 Angle : 0.573 10.473 39759 Z= 0.288 Chirality : 0.045 0.280 4576 Planarity : 0.004 0.050 5108 Dihedral : 4.368 36.073 3890 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3565 helix: 1.27 (0.20), residues: 733 sheet: -0.68 (0.18), residues: 862 loop : -1.52 (0.14), residues: 1970 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 3.700 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 171 average time/residue: 0.3883 time to fit residues: 115.0929 Evaluate side-chains 164 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2558 time to fit residues: 7.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 162 optimal weight: 7.9990 chunk 237 optimal weight: 0.5980 chunk 358 optimal weight: 6.9990 chunk 330 optimal weight: 30.0000 chunk 285 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 220 optimal weight: 20.0000 chunk 175 optimal weight: 0.3980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 29214 Z= 0.269 Angle : 0.584 10.313 39759 Z= 0.295 Chirality : 0.045 0.285 4576 Planarity : 0.004 0.048 5108 Dihedral : 4.446 36.105 3890 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3565 helix: 1.21 (0.20), residues: 732 sheet: -0.64 (0.18), residues: 862 loop : -1.52 (0.14), residues: 1971 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 163 time to evaluate : 3.502 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 165 average time/residue: 0.3656 time to fit residues: 105.4897 Evaluate side-chains 159 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 3.710 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2783 time to fit residues: 6.4606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 263 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 293 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 394 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 185 ASN B 437 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.143584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.097082 restraints weight = 75492.311| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.89 r_work: 0.3258 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 29214 Z= 0.183 Angle : 0.549 10.710 39759 Z= 0.276 Chirality : 0.044 0.271 4576 Planarity : 0.004 0.048 5108 Dihedral : 4.284 35.577 3890 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3565 helix: 1.32 (0.20), residues: 739 sheet: -0.61 (0.18), residues: 870 loop : -1.43 (0.14), residues: 1956 =============================================================================== Job complete usr+sys time: 5288.67 seconds wall clock time: 97 minutes 58.81 seconds (5878.81 seconds total)